A man seen showing someone what was thought to be a handgun at one of Auckland's busiest train stations sparked a cross-city police response today - including armed police stopping and searching a train.

Armed police were called to the Britomart Transport Centre in downtown Auckland and the Glen Innes Train Station in East Auckland after a member of the public reported seeing a man with a handgun near the Britomart station about 5.20pm.

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Auckland Police District Commander Richard Chambers said it was believed the man had boarded the train to Glen Innes, where it was stopped and searched by armed police.

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However, security at the Britomart station located him still inside the Queen St station and he was taken into police custody.

The 22-year-old man was arrested and charges of carrying an imitation fire arm were likely, said Mr Chambers.

"Police have responded pretty well to work with the public and security to resolve the situation quickly," he said.

"Nobody was hurt and we are now speaking to the person concerned to see what their explanation is."

Commuters were quick to talk about the incident on social media - expressing concern about the large presence of armed police at both stations.

A passenger on the Glen Innes-bound train, who did not wish to be identified, said an announcement on the loud speakers alerted passengers to the situation.

"We were stopped [at Glen Innes] for an abnormally long time. After about five minutes they closed the doors to the train, and there was an announcement.

"We were stopped there for about 10 more minutes, and out the window there were a couple of police cars with their lights flashing and I saw a few officers either walking the platform with a security guard or jogging nearby."

Mr Chambers said the Glen Innes-bound train was stopped for about 10-minutes and searched.

"Any situation of this sort is taken very seriously and whilst the person's actions may not have been intended to alarm it's unwise to behave this way - it causes alarm to the public and to the police."

"I understand he showed it to somebody but he was not behaving in an alarming way, but the fact he was carrying it caused alarm."

The gun was not loaded and the man was not using it in a threatening way, said Mr Chambers.

An Auckland Transport spokesman said the train was only stopped for a few minutes and any disruptions were "minor".